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- PDB-6gfs: Thermodynamic, Crystallographic and Computational Studies of Non ... -

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Basic information

Entry
Database: PDB / ID: 6gfs
TitleThermodynamic, Crystallographic and Computational Studies of Non Mammalian Fatty Acid Binding to Bovine b-Lactoglobulin
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lactoglobulin / fatty acid / Non-Mammalian
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PENTADECANOIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKontopidis, G. / Rovoli, M.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Thermodynamic, crystallographic and computational studies of non-mammalian fatty acid binding to bovine beta-Lactoglobulin.
Authors: Rovoli, M. / Thireou, T. / Choiset, Y. / Haertle, T. / Sawyer, L. / Eliopoulos, E. / Kontopidis, G.
History
DepositionMay 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5793
Polymers18,3011
Non-polymers2782
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-7 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.277, 53.277, 111.091
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18301.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LGB / Production host: Bos taurus (domestic cattle) / Tissue (production host): milk / References: UniProt: P02754
#2: Chemical ChemComp-F15 / PENTADECANOIC ACID


Mass: 242.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.495 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein 20 mg/mL, ligand 10mM, 20mM Tris buffer, pH 8, which were mixed with 4 microliter of well solution. Drops were equilibrated against 1 mL of well solution containing 1.43 M sodium ...Details: protein 20 mg/mL, ligand 10mM, 20mM Tris buffer, pH 8, which were mixed with 4 microliter of well solution. Drops were equilibrated against 1 mL of well solution containing 1.43 M sodium citrate and 0.1M Hepes, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.932 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 2→14.8 Å / Num. obs: 12951 / % possible obs: 99.1 % / Redundancy: 15.6 % / Net I/σ(I): 5
Reflection shellResolution: 2→2.03 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→14.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.557 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.171 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 550 4.3 %RANDOM
Rwork0.1927 ---
obs0.19504 12220 98.89 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 44.559 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 2→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 18 83 1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141329
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171284
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.6661797
X-RAY DIFFRACTIONr_angle_other_deg0.9511.6693019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0925163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03725.86258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.22815255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.841153
X-RAY DIFFRACTIONr_chiral_restr0.0680.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021431
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02209
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3752.391652
X-RAY DIFFRACTIONr_mcbond_other2.3722.389651
X-RAY DIFFRACTIONr_mcangle_it3.983.57815
X-RAY DIFFRACTIONr_mcangle_other3.983.571816
X-RAY DIFFRACTIONr_scbond_it2.5862.735674
X-RAY DIFFRACTIONr_scbond_other2.5842.737675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.053.986982
X-RAY DIFFRACTIONr_long_range_B_refined7.62823.8241033
X-RAY DIFFRACTIONr_long_range_B_other7.53923.3951022
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 42 -
Rwork0.243 887 -
obs--98.72 %
Refinement TLS params.Method: refined / Origin x: 15.327 Å / Origin y: -3.784 Å / Origin z: 58.888 Å
111213212223313233
T0.1331 Å2-0.0585 Å20.0021 Å2-0.0675 Å2-0.002 Å2--0.0238 Å2
L2.3334 °20.3903 °2-1.1806 °2-3.8274 °2-0.8325 °2--5.9167 °2
S-0.1749 Å °0.2555 Å °0.1639 Å °-0.2427 Å °0.1058 Å °0.0421 Å °-0.1618 Å °-0.3889 Å °0.0692 Å °

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